Polygenic Score (PGS) ID: PGS000483

Predicted Trait
Reported Trait Breast cancer (female)
Mapped Trait(s) breast carcinoma (EFO_0000305)
Additional Trait Information PheCode 174.1
Released in PGS Catalog: Dec. 15, 2020
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRSWEB_PHECODE174.1_C50_LASSOSUM_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 4,047
Development Method
Name Lassosum
Parameters s=0.5;Lambda=0.01833
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
388,348 individuals (100%)
Score Development/Training
European: 100%
7,368 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
[
  • 8,246 cases
  • , 185,928 controls
]
European
[
  • 1,449 cases
  • , 192,725 controls
]
European
Score Development/Training
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PheCode:174.1; ICD9CM:174.0, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233.0, V10.3; ICD10CM:C50, C50.0, C50.01, C50.011, C50.012, C50.019, C50.02, C50.021, C50.022, C50.029, C50.1, C50.11, C50.111, C50.112, C50.119, C50.12, C50.121, C50.122, C50.129, C50.2, C50.21, C50.211, C50.212, C50.219, C50.22, C50.221, C50.222, C50.229, C50.3, C50.31, C50.311, C50.312, C50.319, C50.32, C50.321, C50.322, C50.329, C50.4, C50.41, C50.411, C50.412, C50.419, C50.42, C50.421, C50.422, C50.429, C50.5, C50.51, C50.511, C50.512, C50.519, C50.52, C50.521, C50.522, C50.529, C50.6, C50.61, C50.611, C50.612, C50.619, C50.62, C50.621, C50.622, C50.629, C50.8, C50.81, C50.811, C50.812, C50.819, C50.82, C50.821, C50.822, C50.829, C50.9, C50.91, C50.911, C50.912, C50.919, C50.92, C50.921, C50.922, C50.929, D05, D05.0, D05.00, D05.01, D05.02, D05.1, D05.10, D05.11, D05.12, D05.8, D05.80, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92
[
  • 1,264 cases
  • , 6,104 controls
]
European MGI

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001168 PSS000549|
European Ancestry|
7,785 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Breast cancer [female] OR: 1.404 [1.322, 1.491]
β: 0.339 (0.0308)
AUROC: 0.595 [0.579, 0.61] Nagelkerke's Pseudo-R²: 0.0264
Brier score: 0.137
Odds Ratio (OR, top 1% vs. Rest): 2.05 [1.3, 3.24]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE174.1_C50_LASSOSUM_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000549 PheCode:174.1; ICD9CM:174.0, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233.0, V10.3; ICD10CM:C50, C50.0, C50.01, C50.011, C50.012, C50.019, C50.02, C50.021, C50.022, C50.029, C50.1, C50.11, C50.111, C50.112, C50.119, C50.12, C50.121, C50.122, C50.129, C50.2, C50.21, C50.211, C50.212, C50.219, C50.22, C50.221, C50.222, C50.229, C50.3, C50.31, C50.311, C50.312, C50.319, C50.32, C50.321, C50.322, C50.329, C50.4, C50.41, C50.411, C50.412, C50.419, C50.42, C50.421, C50.422, C50.429, C50.5, C50.51, C50.511, C50.512, C50.519, C50.52, C50.521, C50.522, C50.529, C50.6, C50.61, C50.611, C50.612, C50.619, C50.62, C50.621, C50.622, C50.629, C50.8, C50.81, C50.811, C50.812, C50.819, C50.82, C50.821, C50.822, C50.829, C50.9, C50.91, C50.911, C50.912, C50.919, C50.92, C50.921, C50.922, C50.929, D05, D05.0, D05.00, D05.01, D05.02, D05.1, D05.10, D05.11, D05.12, D05.8, D05.80, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92
[
  • 1,341 cases
  • , 6,444 controls
]
European MGI